Factors influencing distributional shifts and abundance at the range core of a climate-sensitive mammal

Genomic Vulnerability of a Sentinel Mammal Under Climate Change

Climate change poses a significant threat to biodiversity, particularly in alpine ecosystems where species have already undergone elevational range shifts. Genomics can be used to estimate the adaptive potential of species, as well as the shift in adaptive genomic composition necessary for populations to adjust to climate change (e.g., genomic offset). Here, we investigated patterns of climate-mediated adaptive genetic variation and predicted the degree of genomic offset under multiple climate change scenarios for a sentinel alpine mammal, the American pika (Ochotona princeps). We collected genome-wide data (29,709 SNPs) from 363 individuals spanning the entire range in western North America and employed genotype-environment association analyses to identify 924 robust outlier SNPs, several of which were linked to genes previously associated with high elevation and hypoxia responses in various pika species (Ochotonidae). Adaptive genomic variation was most strongly influenced by mean warmest month temperature, followed by precipitation of the coldest quarter. Spatial patterns of genomic offset were heterogeneous, significantly predicted by levels of adaptive genetic variation, elevation and latitude. Sites within the Northern Rocky Mountains exhibited the highest genomic offset under projected climate change despite possessing high levels of adaptive genetic variation. As such, while our study provides an example of how genomic data can be used to explore the potential consequences of climate change, it further highlights the need for careful consideration of genomic offset values within their proper ecological context.

A New SDM-Based Approach for Assessing Climate Change Effects on Plant-Pollinator Networks

Current methods for studying the effects of climate change on plants and pollinators can be grouped into two main categories. The first category involves using species distribution models (SDMs) to generate habitat suitability maps, followed by applying climate change scenarios to predict the future distribution of plants and pollinators separately. The second category involves constructing interaction matrices between plants and pollinators and then either randomly removing species or selectively removing generalist or specialist species, as a way to estimate how climate change might affect the plant-pollinator network. The primary limitation of the first approach is that it examines plant and pollinator distributions separately, without considering their interactions within the context of a pollination network. The main weakness of the second approach is that it does not accurately predict climate change impacts, as it arbitrarily selects species to remove without knowing which species will truly shift, decline, or increase in distribution due to climate change. Therefore, a new approach is needed to bridge the gap between these two methods while avoiding their specific limitations. In this context, we introduced an innovative approach that first requires the creation of binary climate suitability maps for plants and pollinators, based on SDMs, for both the current and future periods. This step aligns with the first category of methods mentioned earlier. To assess the effects of climate change within a network framework, we consider species co-overlapping in a geographic matrix. For this purpose, we developed a Python program that overlays the binary distribution maps of plants and pollinators, generating interaction matrices. These matrices represent potential plant-pollinator interactions, with a '0' indicating no overlap and a '1' where both species coincide in the same cell. As a result, for each cell within the study area, we can construct interaction matrices for both the present and future periods. This means that for each cell, we can analyze at least two pollination networks based on species co-overlap. By comparing the topology of these matrices over time, we can infer how climate change might affect plant-pollinator interactions at a fine spatial scale. We applied our methodology to Chile as a case study, generating climate suitability maps for 187 plant species and 171 pollinator species, resulting in 2906 pollination networks. We then evaluated how climate change could affect the network topology across Chile on a cell-by-cell basis. Our findings indicated that the primary effect of climate change on pollination networks is likely to manifest more significantly through network extinctions, rather than major changes in network topology.

Evidence of Intraspecific Adaptive Variation in the American Pika (Ochotona princeps) on a Continental Scale Using a Target Enrichment and Mitochondrial Genome Skimming Approach

Montane landscapes present an array of abiotic challenges that drive adaptive evolution amongst organisms. These adaptations can promote habitat specialisation, which may heighten the risk of extirpation from environmental change. For example, higher metabolic rates in an endothermic species may contribute to heightened cold tolerance, whilst simultaneously limiting heat tolerance. Here, using the climate-sensitive American pika (Ochotona princeps), we test for evidence of intraspecific adaptive variation amongst environmental gradients across the Intermountain West of North America. We leveraged results from previous studies on pika adaptation to generate a custom nuclear target enrichment design to sequence several hundred candidate genes related to cold, hypoxia and dietary detoxification. We also applied a 'genome skimming' approach to sequence mitochondrial DNA. Using genotype-environment association tests, we identified rare genomic variants associated with elevation and temperature variation amongst populations. Amongst mitochondrial genes, we identified intraspecific variation in selective signals and significant changes to the amino acid property equilibrium constant, which may relate to electron transport chain efficiency. These results illustrate a complex dynamic of adaptive variation amongst O. princeps where lineages and populations have adapted to unique regional conditions. Some of the clearest signals of selection were in a genetic lineage that includes pikas of the Great Basin region, which is also where recent localised extirpations have taken place and highlights the risk of losing adaptive alleles during environmental change.

Assessing climate niche similarity between persian fallow deer (Dama mesopotamica) areas in Iran

The Persian fallow deer or Mesopotamian fallow Deer (Dama mesopotamica, Brook 1875), a species of significant ecological importance, had faced the threat of extinction in Iran. One conservation strategy involved the translocation of Persian deer to enclosed areas across Iran, where they were afforded protection from external threats and provided with essential care by human caretakers. While human caretakers diligently attend to their needs and mitigate external threats, climate variables may now become critical factors affecting population dynamics in enclosed areas. This study aims to assess the similarity in climate niches between the original area (Dez and Karkheh) of the Persian deer species and 11 newly enclosed areas. To achieve this, we employed climate data and ecological niche modeling (ENM) techniques to assess the variations in climate among 12 areas. We utilized the environmental equivalency test to determine whether the environmental spaces of area pairs exhibit significant differences and whether these spaces are interchangeable. Extrapolation analyses were also constructed in the next steps to explore climatic conditions in original fallow deer habitats that are non-analogous to those in other parts of Iran. Our results reveal significant disparities in climate conditions between the original and all translocated areas. Based on observations of population growth in specific enclosed areas where translocated deer populations have thrived, we hypothesize that the species may demonstrate a non-equilibrium distribution in Iran. Consequently, these new areas could potentially be regarded as part of the species' potential climate niche. Extrapolation analysis showed that for a significant portion of Iran, extrapolation predictions are highly uncertain and potentially unreliable for the translocation of Persian fallow deer. However, the primary objective of translocation efforts remains the establishment of self-sustaining populations of Persian deer capable of thriving in natural areas beyond enclosed areas, thus ensuring their long-term survival and contributing to preservation efforts. Evaluating the success of newly translocated species requires additional time, with varying levels of success observed. In cases where the growth rate of the species in certain enclosed areas falls below expectations, it is prudent to consider climate variables that may contribute to population declines. Furthermore, for future translocations, we recommend selecting areas with climate similarities to regions where the species has demonstrated growth rates.

Evaluating ecosystem protection and fragmentation of the world's major mountain regions

Conserving mountains is important for protecting biodiversity because they have high beta diversity and endemicity, facilitate species movement, and provide numerous ecosystem benefits for people. Mountains are often thought to have lower levels of human modification and contain more protected area than surrounding lowlands. To examine this, we compared biogeographic attributes of the largest, contiguous, mountainous region on each continent. In each region, we generated detailed ecosystems based on Köppen-Geiger climate regions, ecoregions, and detailed landforms. We quantified anthropogenic fragmentation of these ecosystems based on human modification classes of large wild areas, shared lands, and cities and farms. Human modification for half the mountainous regions approached the global average, and fragmentation reduced the ecological integrity of mountain ecosystems up to 40%. Only one-third of the major mountainous regions currently meet the Kunming-Montreal Global Biodiversity Framework target of 30% coverage for all protected areas; furthermore, the vast majority of ecosystem types present in mountains were underrepresented in protected areas. By measuring ecological integrity and human-caused fragmentation with a detailed representation of mountain ecosystems, our approach facilitates tracking progress toward achieving conservation goals and better informs mountain conservation.

Lake Superior's summer cooling of shorelines and adjacent inland forests: Implications for refugia of boreal forests and disjunct arctic-alpine plants

Climate refugia can serve as remnant habitat for cold-adapted species and delay forest transitions. The world's largest freshwater lake by surface area, Lake Superior, serves as a model system for understanding cooling-mediated refugia effects, as its cool summer water temperatures have maintained disjunct populations of arctic-alpine plants on its shoreline since deglaciation. It is known to affect local inland climates by providing a summer cooling effect; however, the inland temperature gradient and spatial patterns of cooling have not been well quantified. Here, we describe the extent, degree, and patterns of temperature buffering and examine drivers of buffering and disjunct plant occurrence for Lake Superior's north shore over a 3-year period at distances of 10, 100 m, 1, 10, and 100 km inland. We analyzed temperature data by year, month, summer maximum (July), and growing degree days (GDD0) for each site. Average summertime cooling at shore sites (10 m) was ~5°C cooler than reference sites (100 km inland), with a maximum difference of -19.2°C. The magnitude of cooling varied geographically, with sites further west and southeast showing little to no cooling effect, while the exposed north-central shore showed the highest degree of buffering (5.8°C cooler) and had a shorter growing season than reference sites. Finally, north-central shorelines had fewer days above 16°C, a threshold above which disjunct plants are unlikely to grow. These sites also showed the highest proportion of disjunct arctic-alpine species, reflecting the highest buffering from inland sites. On north-central shores, sites up to 10 km inland had less than 10 days per year warmer than 20°C, a threshold identified for boreal forest transition. An understanding of the extent of lake-mediated cooling on adjacent forests can better inform the risk to disjunct species, inland forests, and vegetation transition models on Lake Superior's north shore.

Assessing Surveillance of Wildlife Diseases by Determining Mammal Species Vulnerability to Climate Change

Climate change is one of the drivers of wildlife-borne disease emergence, as it can affect species abundance and fitness, host immunocompetence, and interactions with pathogens. To detect emerging wildlife-borne diseases, countries may implement general wildlife-disease surveillance systems. Such surveillance exists in the Netherlands. However, it is unclear how well it covers host species vulnerable to climate change and consequently disease emergence in these species. Therefore, we performed a trait-based vulnerability assessment (TVA) to quantify species vulnerability to climate change for 59 Dutch terrestrial mammals. Species' vulnerability was estimated based on the magnitude of climatic change within the species' distribution (exposure), the species' potential to persist in situ (sensitivity), and the species' ability to adjust (adaptive capacity). Using these vulnerability categories, we identified priority species at risk for disease emergence due to climate change. Subsequently, we assessed the frequency of occurrence of these priority species compared to other mammal species examined in general wildlife disease surveillance during 2008-2022. We identified 25% of the mammal species to be highly exposed, 24% to be highly sensitive, and 22% to have a low adaptive capacity. The whiskered myotis and the garden dormouse were highly vulnerable (i.e., highly exposed, highly sensitive, and low adaptive capacity), but they are rare in the Netherlands. The Western barbastelle, the pond bat, and the Daubenton's myotis were potential adapters (highly exposed, highly sensitive, and high adaptive capacity). Species vulnerable to climate change were relatively poorly represented in current general surveillance. Our research shows a comprehensive approach that considers both exposures to climate change and ecological factors to assess vulnerability. TVAs, as presented in this study, can easily be adapted to include extra drivers and species, and we would therefore recommend surveillance institutes to consider integrating these types of assessments for evaluating and improving surveillance for wildlife-borne disease emergence.

Giant pandas are losing their edge: Population trend and distribution dynamic drivers of the giant panda

Comprehending the population trend and understanding the distribution range dynamics of species are necessary for global species protection. Recognizing what causes dynamic distribution change is crucial for identifying species' environmental preferences and formulating protection policies. Here, we studied the rear-edge population of the flagship species, giant pandas (Ailuropoda melanoleuca), to (1) assess their population trend using their distribution patterns, (2) evaluate their distribution dynamics change from the second (1988) to the third (2001) survey (2-3 Interval) and third to the fourth (2013) survey (3-4 Interval) using a machine learning algorithm (eXtremely Gradient Boosting), and (3) decode model results to identify driver factors in the first known use of SHapley Additive exPlanations. Our results showed that the population trends in Liangshan Mountains were worst in the second survey (k = 1.050), improved by the third survey (k = 0.97), but deteriorated by the fourth survey (k = 0.996), which indicates a worrying population future. We found that precipitation had the most significant influence on distribution dynamics among several potential environmental factors, showing a negative correlation between precipitation and giant panda expansion. We recommend that further research is needed to understand the microenvironment and animal distribution dynamics. We provide a fresh perspective on the dynamics of giant panda distribution, highlighting novel focal points for ecological research on this species. Our study offers theoretical underpinnings that could inform the formulation of more effective conservation policies. Also, we emphasize the uniqueness and importance of the Liangshan Mountains giant pandas as the rear-edge population, which is at a high risk of population extinction.

Animal conflicts escalate in a warmer world

The potential for climate change to affect animal behaviour is widely recognized, yet its possible consequences on aggressiveness are still unclear. If warming and drought limit the availability of food resources, climate change may elicit an increase of intraspecific conflicts stemming from resource competition. By measuring aggressivity indices in a group-living, herbivorous mammal (the Apennine chamois Rupicapra pyrenaica ornata) in two sites differing in habitat quality, and coupling them with estimates of plant productivity, we investigated whether harsh climatic conditions accumulated during the growing season influenced agonistic contests at feeding via vegetation-mediated effects, and their interaction with the site-specific habitat quality. We focused on females, which exhibit intra-group contest competition to access nutritious food patches. Accounting for confounding variables, we found that (1) the aggression rate between foraging individuals increased with the warming accumulated over previous weeks; (2) the probability to deliver more aggressive behaviour patterns toward contestants increased with decreasing rainfall recorded in previous weeks; (3) the effects of cumulative warming and drought on aggressivity indices occurred at time windows spanning 15-30 days, matching those found on vegetation productivity; (4) the effects of unfavourable climatic conditions via vegetation growth on aggressivity were independent of the site-specific habitat quality. Simulations conducted on our model species predict a ~50 % increase in aggression rate following the warming projected over the next 60 years. Where primary productivity will be impacted by warming and drought, our findings suggest that the anticipated climate change scenarios may trigger bottom-up consequences on intraspecific animal conflicts. This study opens the doors for a better understanding of the multifactorial origin of aggression in group-living foragers, emphasising how the escalation of agonistic contests could emerge as a novel response of animal societies to ongoing global warming.

Global change effects on Mediterranean small mammal population dynamics: Demography of Algerian mice (Mus spretus) along land use and climate gradients

Climate and land use change are key global change drivers shaping future species' distributions and abundances. Negative interactions among effects of drivers can reduce the accuracy of models aimed at predicting such distributions. Here we analyse how climate and land use affected population dynamics and demography of the Algerian mouse (Mus spretus), an open-land thermophilic Mediterranean small mammal. Change to a warmer and drier climate would facilitate the expansion of the species, whereas landscape change (forest encroachment following extensive land abandonment) would produce its retreat. We correlated abundance and demography parameters computed from captures obtained in 16 plots during a 10-years period (2008-2017; SEMICE small mammal monitoring) with climate, vegetation and land use change. Climate became warmer and dryer, and afforestation due to encroachment occurred in 81 % of plots. Expected positive effects of climate warming, derived from bioclimatic niche models, were counterbalanced by negative effects of both increasing hydric deficit and changes in vegetation and landscape structure. Abundance showed a slight but significant decline (-5 %). The species' range was more resilient to change, as shown by occupancy analyses, apparently due to strong local effects of vegetation structure on occupancy. This result highlighted that negative population trends would not necessarily produce range retractions. Simultaneously analysing both abundance trends and occupancy patterns may thus allow for deeper understanding and more accurate predictions of expected population trends in response to interacting global change drivers.

Small mammals in a mountain ecosystem: the effect of topographic, micrometeorological, and biological correlates on their community structure

An increasing number of studies have investigated spatial and temporal patterns in species richness and assemblage composition in mountain ecosystems along altitudinal gradients. Small mammals have been successfully used as indicators of environmental health and as proxies of biodiversity. However, information about the composition and distribution of species assemblages in the mosaic of habitat and rocky landform types at a high altitude is still lacking for most of the mountain regions. Through the use of live traps and camera trapping, we described the small mammal community living above the treeline of the Western Dolomites (Italian Alps), investigating the species richness, abundance of individuals and community composition in relation to topographic, micrometeorological, mesohabitat, and biological correlates. A total of five species and 50 individuals were sampled, analysed, and released. At the extremes of the analysed altitudinal range (i.e. 1900 vs 2900 m a.s.l.), community composition was completely different and species richness was related to elevation, steepness, and vegetation cover. At the same time, the taxonomic distinctness of ground-dwelling arthropods (namely carabid beetles and spiders), a proxy of habitat complexity, showed higher values in areas with a greater small mammal species richness. We found a positive effect of steepness and rocky landform type “carsism” on the number of captured individuals, showing the importance of the availability of shelters and underground burrows for the sampled species. As a confirmation of the altitudinal shift for these species in relation to the ongoing climate change, we detected a negative impact of sub-surface ground temperature on small mammal abundance during the monitoring period. In conclusion, small mammals represent an excellent model for understanding the evolutionary processes of ecosystems, population dynamics under changing environmental conditions, and habitat vulnerabilities.

Human populations in the world’s mountains: Spatio-temporal patterns and potential controls

Changing climate and human demographics in the world’s mountains will have increasingly profound environmental and societal consequences across all elevations. Quantifying current human populations in and near mountains is crucial to ensure that any interventions in these complex social-ecological systems are appropriately resourced, and that valuable ecosystems are effectively protected. However, comprehensive and reproducible analyses on this subject are lacking. Here, we develop and implement an open workflow to quantify the sensitivity of mountain population estimates over recent decades, both globally and for several sets of relevant reporting regions, to alternative input dataset combinations. Relationships between mean population density and several potential environmental covariates are also explored across elevational bands within individual mountain regions (i.e. “sub-mountain range scale”). Globally, mountain population estimates vary greatly—from 0.344 billion (<5% of the corresponding global total) to 2.289 billion (>31%) in 2015. A more detailed analysis using one of the population datasets (GHS-POP) revealed that in ∼35% of mountain sub-regions, population increased at least twofold over the 40-year period 1975–2015. The urban proportion of the total mountain population in 2015 ranged from 6% to 39%, depending on the combination of population and urban extent datasets used. At sub-mountain range scale, population density was found to be more strongly associated with climatic than with topographic and protected-area variables, and these relationships appear to have strengthened slightly over time. Such insights may contribute to improved predictions of future mountain population distributions under scenarios of future climatic and demographic change. Overall, our work emphasizes that irrespective of data choices, substantial human populations are likely to be directly affected by—and themselves affect—mountainous environmental and ecological change. It thereby further underlines the urgency with which the multitudinous challenges concerning the interactions between mountain climate and human societies under change must be tackled.